L1-4 Flashcards
PATHOGENS
organisms causing disease
immune system requirements
recognition and response
correct reaction to benign/ self
direction of effector mechanisms to specific pathogens
adapative and innate linkage
infection sources
pathogens
bacteria
fungi
parasites (worms/ protozoa)
specific immunity features
lymphocyte mediation
clonal dist. of receptors
large repertoire/ low freq specific cells for antigen
slow response development of memory cells
clonal selection theory
clonal deletion of self-reactive immature lymphocytes
mature naive lymphocytes proliferate and differentiate upon activation
effector cells clones
BCR
expressed by B cells upon antibody activation
Ig membrane form binds free antigen
TCR
membrane-form only
recognizes peptide fragment of antigen bound to MHC on APC
bacterial infection response
complement activation> opsonization/ classical pathway activation/ effector cell activation
FcR cells
receptor binding Fc antibody region
antibody structure
4 polypeptides
paired variable regions
constant regions > form Fc regions/ receptors
heavy/ light chain
antibody classes
IgM/D/A/G/E
What are antibody classes determined by
heavy chain/ C region
no. homology regions in L/H regions
L>2
H>4/5
homology domain
110 amino acids
2 beta sheets
disulphide bridge link
paired (folded in protein)
antibody antigen interaction
variable region specific to antibodies
6 hypervariable loops (3Vh/Vl) act as Ag binding sites > 12 regions
CDR on antibody
complementarity defining regions
> determines specificity/ affinity for Ag
antigen binding of CDRs
Ag bind amino acids in complementarity defining regions
epitope
antibody recognition site on an antigen
2 types of epitope
linear/ continuous
non-linear
Ag/Ab interactions nature
non-covalent
TCR
binds processed antigens in cleft of MHC I/II (Peptide-MHC complex)
Membrane-bound
smaller than BCR
TCR structure
alpha/ beta chain heterodimer
V/C regions (V peptide bound)
4 Ig-like domains
3 CDR’s
HLA
human leukocyte antigens
A/B/C alpha chains
class I/II
on ch6
7*10^6 bp
class I MHC
single chain
expressed by all nuc cells
alpha/ beta 2 microglobulin
bind peptides 8-10 amino acids for TCR presentation
class II MHC
alpha/ beta chain heterodimer expressed on APC
expressed by immune cells
binds peptides 13+ amino acids
variation in MHC class I/II
highly polymorphic
limited variation in one individual
variation of TCR
highly variable
clonally distributed
antibody
H2L2
secreted/ expressed on B cells
binds free Ag
variability of antibodies
highly variable
clonally distributed
alpha 2/ beta 2 coding
Ig-like
alpha 1/ beta 1
peptide binding site
MHC 1 vs II groove length
groove II is more open than I as binds longer peptides
co-expression of TCR recognizing class I
CD8+ killer T
co-expression of TCR recognizing class II
CD4+ helper T
whats the V region of the heavy chain Ig encoded by
V/D/J segments
V (Variable) D (diversity) J(joining)
V is biggest segment
What’s the light chain variable region encoded by?
V/J
less variability than heavy chain > V/d/J
Which T cell receptor is the heavy vs light chain?
Heavy chain = TCR alpha
light chain = TCR beta
B cell gene rearrangements
in bone marrow development
NHEJ
Non-homologous end joining
DNA repair ligating DNA pairs
light chain genes
lamda/ kappa
Loci of H/ lamda/ kappa genes
H- 14
lamda- 2
kappa- 22
recombination signal sequences
sequences flanking V/D/J gene segments
V/D/J recombinases
recombination activating genes 1/2 encoding lymphoid specific components of recombinase
RAG mutations consequences
recombination activating gene
immunodeficiences
Allelic exclusion
per B> 1 rearranged H and 1 rearranged L chain per chromosomes therefore randomly generated BCR
kappa OR lamda light chain never both
mechanisms for allelic exclusion
- multiple gene segments/ chain
- combinatorial diversity
- H/L chain combinations
- junctional diversity
- somatic hypermutations
2. V/D/J segment recomination
junctional diversity
imprecise joining
N regions
random nuc additions at junctions via terminal transferase
SHM
somatic hypermutation
mutation frequency in antibody H/ lamda/ kappa genes at orders of magnitude higher than others
in germinal centers as B recognize Ag asnd proliferate
AID
Activation induced deaminase
deaminates DNA cytosine to uracil which is recognized
Mechanism induced by B recognition of Ag
secrete unique BCR as Ig with alternate constant region w/o transmembrane region
both produced by alternative RNA processing
heavy chain constant region genes
4* gamma chain gene
2*alpha chain gene segments
C mu closest to V/D/J gene segments
IgM
1st class isotype BCR/ antibody expressed by each developing B cell
co-expressed with IgD
TCR gene segment rearrangement
when/ where
how is it similar to Ig gene rearrangement?
During T development in thymus
similar to Ig gene rearrangement> RSS/ RAG enzymes involved
diversity of TCR rearrangement
- multiple gene segments
- combinatorial diversity
- junctional diversity
no SHM in TCRs
TCR alpha/beta chromosomes
alpha-14
beta- 7
where do TCR’s recognize antigens
in groove of MHC moelcule
MHC diversity
major histocompatibility complex
which chromosome is HLA gene found on?
no gene rearrangement
co-dominant expression
most polymorphic genes
Ch 6
Co-dominant expression of MHC
Where are these expressed?
MHC I
MHC II
1 in all nucleated cells
II in immune cells
MHC I molecules
MHC class II molecules
No. molecules if heterozygous at each loci?
MHCI> HLA-A/HLA-B/HLA-C
MHCII> HLA-DQ/DP/DR
6
MHC polymorphism
advantages/ disadvantages
:) allows binding of peptide range presented to cells
:( ^risk of immune-mediated disease
:( lower donor organ pool
endogenous/ exogenous Ag-derived peptides
endo> virus (class I presented)
exo> bacterium/ fungus (class II presented)
both processed into fragments for binding/ presentation by MHC I/II
MHC class I presentation
- intra antigen synth in ctoplasm
- Ag processed > peptide by proteasome
- TAP transporter to ER
- pep binding to MHC I
- MHC I presentation at CSM
proteasome
inflam cytokine reception produces altered peptides
large multicatalytic protease
what’s TAP
Multi-protein assembly / peptide loading component
contains tapasin/ calreticulin
TAP functions
cytosolic protein degradation to peptide fragments by proteasome
delivers peptide to MHC Class I and folds for export
MHC class II molecule presentation
- Ag endocytosed via vesicles
- acid proteases cleave protein
- vesicles fuse with MHC II and bind
- complex transported to CSM
invariant chain complex in MHC II
function
blocks peptide/ misfolded protein binding in groove
HLA-DM binds
cleaved in acidified endosome > peptide fragment CLIP enzyme
CLIP function
blocks peptide binding ass. w binding groove
released when HLA-DM binds to MHC II
what happens to peptides in normal, uninfected cells?
MHC I/ II bind and present peptides from self-proteins
class I/II MHC accessory molecules encoded
class I> TAP/LMP
class II> HLA-DM
where are B cells and plasma cells found?
in bone marrow
gene controlling B cell identity
Pax5
B cell development
- develop from haematopoietic stem cells in bone marrow
- express PAX5 txn factor
- Ig gene rearrangement
- lymphocyte then B cell- specific markers expressed
- negative selection of self-reactive cells
Pre-B cell development
immature pre-B cells
- H chain genes rearrange to cell surface with Igalpha/beta> expressed with surrogate light chain
produces a pre B cell receptor - L chains rearrange > displace V pre-B / lamda 5 genes and producing IgM BCR
H chain = mu chain
Pre-B cell receptor function
delivers signal to pre-B cells that H chain is functional nctional
no antigen required
Pre-BCR signal
- turns off RAG1/RAG2
- 5-6 cell divisions
- surrogate light chain expression stops
- RAG1/2 turned on again
- L chain rearrangement
L chain rearrangement requires RAG
Ig alpha/ beta function
mediate signalling of immature B cells
B cell names during development
stem cell> early pro B cell> pro B cell> large pre-B cell> small pre B cell> immature B cell> mature B cell
light chain posiibilities from pre-B cells
lamda or kappa light chain
kappa versus lamda expression on light chains
more kappa than lamda as kappa light chains rearraneg prior to lamda
where are RAG1/2 switched off?
large pre-B cell/ mature B cells
lymphoid specific recombinase
no. J(kappa) genes per chromosome
5 per chromosome
and 2 chromosomes therefore 10 rearrangements possible on same locus
lamda locus will then rearrange if all 10 rearrangements are out of frame
Ig rearrangement errors consequences
failure to productively rearrange H and L chains result in cell death
Ig rearrangement sequence
D-J on both chromosomes
V-DJ on 1/2 chromosomes
kappa gene rearrangement (up to 5 times) on 1/2 chromosomes> rearrangement of lamda if kappa fails on 1/2 chromosomes
mu: kappa/lamda expressed
Ig expressed in immature B cells
membrane IgM
what happens to immature B cells binding multivalent self-antigens?
clonal deletion
receptor editing
receptor ediitng entails further light chain rearrangements/ variable ge
what happens to immature B cells binding soluble self-antigens?
become anergic/ unresponsive
T cell development
Develop from bone marrow stem cells
receptor genes rearranged in thymus
pre-T receptor expressed
negative selection of self-reactive T cells
T cell alternative lineages
alpha beta TCR genes (CD4+/CD8+)
gamma delta TCR genes
cells expressing alpha beta TCR bind with self MHC expressed in thymus (
alpha beta T cell development
develop into thymocytes in thymus
1. beta TCR genes rearranged and express TCR
2. CD3/4/5 markers acquired\
3. +/- selection
thymus characteristics
bi-lobed organ in anterior mediastinum
outer cortex/ innor medulla per lobule
made up of dendritic/ macrophage/ epithelial / lymphoid cells
pro-thymocytes enter cortex via blood vessels from bone marrow
thymocyte TCR rearrangement
- TCR beta rearranged
- expression w pre-beta receptor
- cell proliferationa nd TCR beta rearrangement
markers expressed w TCR
CD3
CD4 and CD8
peripheral T Cells express either CD4 or CD8
CD3 function
transmits signal to T cell nucleus after TCR recognition of p/ MHC
TCR expression requirements
CD3 complex
delta, epsilon and gamma chains
zeta chain dimer
gamma delta TCR
less diverse TCR
don’t express CD4/CD8
in epithelial tissues at mucosal surfaces
lineage commitment to gamma delta/ alpha beta depends on order of intial rearrangements
immunity T cell recognition
recognize self-MHC + foreign Ag peptide
positively selected and moved to medulla
autoimmunity T cell recognition
Recognize self-MHC + peptide from self
positively selected and moved to medulla prior to removal by negative se
clonal deletion with those with highest affinity for TCR neg. selected
positive selection of T cells
T cells recognize MHC on cortical epithelial cells in thymus
positively selected move to medulla
apoptosis if no recognition
negative selection of T cells
on thymic dendritic cells/ macrophages w high affinityTCR negatively selected
therefore population of T cells w low affinity for self-peptide + self-MHC
CD 8 + T cells
recognize MHC class I Ag
CD4+ T cells
recognize MHC class II Ag
what type of proteins are BCRs?
heterodimeric
Do TCRs recognise carbohydrate?
no
MHC I/II binding groove
I snaps shut on smaller peptides in ER following TAP translocation
II has binding groove blocked by CLIP (removed in endocytic pathway by HLA-DM)
which chain determines an antibody’s isotype?
heavy
